Gene expression is modulated by proteins that bind to specific sequences in the control regions of genes. Once bound, these factors modulate transcription of the DNA into messenger RNA. A transcription factor typically influences the expression of several genes. By identifying these genes, the mechanisms of a cell's response during development, under stress conditions, or while undergoing tumorigenesis may be revealed and investigated.
In order to elucidate these mechanisms, it is necessary to identify the gene targets of the transcription factors that are active in the cell. A variety of methods have been utilized but most are indirect. For example, both subtraction cloning and differential RNA display can be used to obtain cDNAs of genes that are unique to a particular condition in which the transcription factors is present. The disadvantage of these methods is that the genes obtained may not be directly regulated by the transcription factor of interest. The genes mat be controlled by other transcription factors that are induced under the same conditions or that act downstream of the transcription factor of interest. Consequently, the genes identified in these methods may not be part of the regulatory program being investigated. Another process screens DNA arrays to identify the genes that hybridize to RNA prepared from cells which express a particular transcription factor but not to RNA isolated from cells which do not express the transcription factor. Unfortunately, this technique also may not lead to identification of genes under the direct regulation of the transcription factor.
To understand a modulated network, such as a signal transduction pathway, it is important to characterize as many of the genes that are being controlled by the transcription factor as possible. Unfortunately the procedure of isolating the genes from libraries has hindered progress toward identifying a set of genes regulated together by the transcription factor of interest. Screening cDNA libraries by hybridization to obtain genes corresponding to the DNA fragments obtained by a variety of methods requires that each fragment isolated be used individually to screen the library. This is extremely time-consuming, labor-intensive, and costly. Consequently there is a need in the industry to increase the efficiency of obtaining gene targets of transcription factors of interest.